On the Simulation of Conformational Transitions: Smoothing Path Energy Minimization Results

Abstract

Path energy minimization is a method for calculating a quasi-continuous reaction path linking two known conformers of a molecule. Although the method locates the transition state configuration lower energy regions of the path are not optimized. This work examines four methods of following routes downhill from the transition state. Results are compared for the test system of a pucker angle change for the sugar α-D-xylulofuranose. Restrained energy minimization is found to be the superior method. The steepest descents path obtained by this method is shown to be distinct from the route found by adiabatic mapping.

Key Words:

• Molecular mechanics
• sugar conformation
• transition state
• reaction cooridinate
• restrained energy minimization